Multiple sequence alignment - TraesCS3A01G120300

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS3A01G120300 chr3A 100.000 2408 0 0 1 2408 94114651 94117058 0.000000e+00 4447
1 TraesCS3A01G120300 chr3A 95.668 2262 76 9 152 2408 720323632 720321388 0.000000e+00 3615
2 TraesCS3A01G120300 chr3A 95.770 1253 43 5 1164 2408 393190826 393189576 0.000000e+00 2012
3 TraesCS3A01G120300 chr3A 95.913 1101 41 4 1 1099 393191918 393190820 0.000000e+00 1781
4 TraesCS3A01G120300 chr3A 96.774 155 4 1 1 155 720325420 720325267 8.540000e-65 257
5 TraesCS3A01G120300 chr2A 86.357 1957 138 55 1 1917 153034025 153032158 0.000000e+00 2015
6 TraesCS3A01G120300 chr2A 84.088 861 75 29 1 848 385329164 385328353 0.000000e+00 774
7 TraesCS3A01G120300 chr2A 81.703 634 64 12 884 1491 385328358 385327751 4.660000e-132 481
8 TraesCS3A01G120300 chr2A 77.869 488 71 17 1 478 753539634 753540094 3.950000e-68 268
9 TraesCS3A01G120300 chr4B 91.939 1439 65 16 1 1412 652266629 652268043 0.000000e+00 1967
10 TraesCS3A01G120300 chr4B 82.272 1162 125 33 1252 2408 13295278 13296363 0.000000e+00 929
11 TraesCS3A01G120300 chr4B 87.874 701 75 9 1700 2394 652268675 652269371 0.000000e+00 815
12 TraesCS3A01G120300 chr3B 89.606 1597 93 25 1 1566 739845171 739846725 0.000000e+00 1962
13 TraesCS3A01G120300 chr3B 87.177 1279 81 23 330 1576 753928575 753927348 0.000000e+00 1376
14 TraesCS3A01G120300 chr3B 87.074 704 78 12 1700 2394 739846879 739847578 0.000000e+00 784
15 TraesCS3A01G120300 chr3B 87.074 704 78 9 1700 2397 753927198 753926502 0.000000e+00 784
16 TraesCS3A01G120300 chr3B 93.694 333 18 3 1 333 753942685 753942356 1.660000e-136 496
17 TraesCS3A01G120300 chr7A 85.228 1293 116 33 1 1261 533505343 533506592 0.000000e+00 1260
18 TraesCS3A01G120300 chr7A 85.598 861 67 26 1 848 44434599 44435415 0.000000e+00 850
19 TraesCS3A01G120300 chr7A 94.717 530 21 5 1512 2037 732368026 732367500 0.000000e+00 817
20 TraesCS3A01G120300 chr7A 96.512 344 12 0 2065 2408 732367503 732367160 9.660000e-159 569
21 TraesCS3A01G120300 chr7A 81.877 618 58 17 884 1475 44435410 44435999 2.800000e-129 472
22 TraesCS3A01G120300 chr7A 93.855 179 10 1 1260 1437 732368568 732368390 3.950000e-68 268
23 TraesCS3A01G120300 chr7A 78.626 262 28 9 1252 1512 533506608 533506842 5.360000e-32 148
24 TraesCS3A01G120300 chr7B 82.100 1162 125 33 1252 2408 568792980 568794063 0.000000e+00 917
25 TraesCS3A01G120300 chr7B 86.765 476 30 15 1 475 568782518 568782961 1.290000e-137 499
26 TraesCS3A01G120300 chr7B 87.824 386 42 4 572 956 568783645 568784026 4.720000e-122 448
27 TraesCS3A01G120300 chrUn 89.689 708 53 14 288 992 8774039 8773349 0.000000e+00 885
28 TraesCS3A01G120300 chrUn 83.527 862 78 29 1 848 71653890 71654701 0.000000e+00 747
29 TraesCS3A01G120300 chr1D 85.400 863 66 29 1 848 12308202 12309019 0.000000e+00 841
30 TraesCS3A01G120300 chr1D 81.757 592 58 16 926 1491 12309170 12309737 1.310000e-122 449
31 TraesCS3A01G120300 chr3D 85.250 861 68 30 1 848 289812050 289811236 0.000000e+00 832
32 TraesCS3A01G120300 chr3D 81.250 240 19 6 1252 1491 289810736 289810523 1.140000e-38 171
33 TraesCS3A01G120300 chr1B 85.006 827 99 13 1586 2408 663581959 663581154 0.000000e+00 817
34 TraesCS3A01G120300 chr7D 81.307 658 76 20 926 1555 2016337 2015699 7.740000e-135 490
35 TraesCS3A01G120300 chr7D 82.095 592 56 17 926 1491 87752835 87752268 6.070000e-126 460
36 TraesCS3A01G120300 chr6A 80.997 642 78 14 884 1491 437497894 437497263 1.010000e-128 470
37 TraesCS3A01G120300 chr2B 86.007 293 34 7 880 1168 588394872 588395161 8.360000e-80 307


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3A01G120300 chr3A 94114651 94117058 2407 False 4447.000000 4447 100.0000 1 2408 1 chr3A.!!$F1 2407
1 TraesCS3A01G120300 chr3A 720321388 720325420 4032 True 1936.000000 3615 96.2210 1 2408 2 chr3A.!!$R2 2407
2 TraesCS3A01G120300 chr3A 393189576 393191918 2342 True 1896.500000 2012 95.8415 1 2408 2 chr3A.!!$R1 2407
3 TraesCS3A01G120300 chr2A 153032158 153034025 1867 True 2015.000000 2015 86.3570 1 1917 1 chr2A.!!$R1 1916
4 TraesCS3A01G120300 chr2A 385327751 385329164 1413 True 627.500000 774 82.8955 1 1491 2 chr2A.!!$R2 1490
5 TraesCS3A01G120300 chr4B 652266629 652269371 2742 False 1391.000000 1967 89.9065 1 2394 2 chr4B.!!$F2 2393
6 TraesCS3A01G120300 chr4B 13295278 13296363 1085 False 929.000000 929 82.2720 1252 2408 1 chr4B.!!$F1 1156
7 TraesCS3A01G120300 chr3B 739845171 739847578 2407 False 1373.000000 1962 88.3400 1 2394 2 chr3B.!!$F1 2393
8 TraesCS3A01G120300 chr3B 753926502 753928575 2073 True 1080.000000 1376 87.1255 330 2397 2 chr3B.!!$R2 2067
9 TraesCS3A01G120300 chr7A 533505343 533506842 1499 False 704.000000 1260 81.9270 1 1512 2 chr7A.!!$F2 1511
10 TraesCS3A01G120300 chr7A 44434599 44435999 1400 False 661.000000 850 83.7375 1 1475 2 chr7A.!!$F1 1474
11 TraesCS3A01G120300 chr7A 732367160 732368568 1408 True 551.333333 817 95.0280 1260 2408 3 chr7A.!!$R1 1148
12 TraesCS3A01G120300 chr7B 568792980 568794063 1083 False 917.000000 917 82.1000 1252 2408 1 chr7B.!!$F1 1156
13 TraesCS3A01G120300 chr7B 568782518 568784026 1508 False 473.500000 499 87.2945 1 956 2 chr7B.!!$F2 955
14 TraesCS3A01G120300 chrUn 8773349 8774039 690 True 885.000000 885 89.6890 288 992 1 chrUn.!!$R1 704
15 TraesCS3A01G120300 chrUn 71653890 71654701 811 False 747.000000 747 83.5270 1 848 1 chrUn.!!$F1 847
16 TraesCS3A01G120300 chr1D 12308202 12309737 1535 False 645.000000 841 83.5785 1 1491 2 chr1D.!!$F1 1490
17 TraesCS3A01G120300 chr3D 289810523 289812050 1527 True 501.500000 832 83.2500 1 1491 2 chr3D.!!$R1 1490
18 TraesCS3A01G120300 chr1B 663581154 663581959 805 True 817.000000 817 85.0060 1586 2408 1 chr1B.!!$R1 822
19 TraesCS3A01G120300 chr7D 2015699 2016337 638 True 490.000000 490 81.3070 926 1555 1 chr7D.!!$R1 629
20 TraesCS3A01G120300 chr7D 87752268 87752835 567 True 460.000000 460 82.0950 926 1491 1 chr7D.!!$R2 565
21 TraesCS3A01G120300 chr6A 437497263 437497894 631 True 470.000000 470 80.9970 884 1491 1 chr6A.!!$R1 607

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
814 3062 1.463674 CCCACTCATAACAGTTGCCC 58.536 55.0 0.0 0.0 0.0 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1929 5091 2.620242 GAACAAAATACCGCCCGTAGA 58.38 47.619 0.0 0.0 0.0 2.59 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
80 84 9.817809 GACTATCATGAAGTAAACCTGTCAATA 57.182 33.333 0.00 0.0 0.00 1.90
128 132 4.394920 GCTTCGGGATGAGTATTGAAAACA 59.605 41.667 0.00 0.0 0.00 2.83
547 2688 7.810282 CAGTCATACATGCTTATCCTACTGTAC 59.190 40.741 0.00 0.0 0.00 2.90
814 3062 1.463674 CCCACTCATAACAGTTGCCC 58.536 55.000 0.00 0.0 0.00 5.36
833 3081 2.953648 CCCCAACCAAGTTAAGAACGTT 59.046 45.455 0.00 0.0 36.23 3.99
1022 3388 3.724478 TGGGGAGTAACTCACATCAGAT 58.276 45.455 0.00 0.0 35.24 2.90
1301 3702 1.299648 CGGATCCTTGGGCACTTCA 59.700 57.895 10.75 0.0 0.00 3.02
1340 3741 2.193248 GGCCGAGAAGATTGGGGG 59.807 66.667 0.00 0.0 32.21 5.40
1415 3850 2.108250 GCCTGAGGAGGTAGAGAGAGAT 59.892 54.545 0.65 0.0 42.15 2.75
1665 4398 4.379394 CGTCCGATGTTGTCCAATTCATTT 60.379 41.667 0.00 0.0 0.00 2.32
1666 4399 5.469479 GTCCGATGTTGTCCAATTCATTTT 58.531 37.500 0.00 0.0 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
80 84 4.054780 TCAGCGTTGTACAGAAGAAGTT 57.945 40.909 0.00 0.0 0.00 2.66
128 132 2.026641 GCCTGCCATACACATTGACAT 58.973 47.619 0.00 0.0 0.00 3.06
297 1939 5.063880 AGATATATTTCTTGTTGTCCCGGC 58.936 41.667 0.00 0.0 0.00 6.13
547 2688 7.120579 AGGATCAAGAGAAGCATAGTACGATAG 59.879 40.741 0.00 0.0 46.19 2.08
814 3062 6.575942 CGATTAAACGTTCTTAACTTGGTTGG 59.424 38.462 0.00 0.0 0.00 3.77
833 3081 6.032956 TCTTGGAGTAAGCTGTTCGATTAA 57.967 37.500 0.00 0.0 36.31 1.40
1022 3388 6.314648 CACTTCAGCTTTCATATCTGCTTGTA 59.685 38.462 0.00 0.0 33.03 2.41
1415 3850 2.739379 CACAACACACACACACACACTA 59.261 45.455 0.00 0.0 0.00 2.74
1666 4399 4.020543 ACCAAATGCGCTAGGGATAAAAA 58.979 39.130 11.61 0.0 0.00 1.94
1682 4417 6.650390 GCTGAATACAAACCAAATGACCAAAT 59.350 34.615 0.00 0.0 0.00 2.32
1738 4897 4.041567 TCCACATAGTCAAACTGGACACAT 59.958 41.667 0.00 0.0 40.29 3.21
1929 5091 2.620242 GAACAAAATACCGCCCGTAGA 58.380 47.619 0.00 0.0 0.00 2.59


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.